Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

MOTIVATION With the advancements of next-generation sequencing technology, it is now possible to study samples directly obtained from the environment. Particularly, 16S rRNA gene sequences have been frequently used to profile the diversity of organisms in a sample. However, such studies are still taxed to determine both the number of operational taxonomic units (OTUs) and their relative abundan...

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

BACKGROUND High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation along the 16S rRNA gene is only partially captured by short reads. The recen...

Phylogenetic clustering of soil microbial communities by 16S rRNA but not 16S rRNA genes.

We evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly active taxa detected by only rRNA.

Genetic variations of avian Pasteurella multocida as demonstrated by 16S-23S rRNA gene sequences comparison

Pasteurella multocida is known as an important heterogenic bacterial agent causes some severe diseases such as fowl cholera in poultry and haemorrhagic septicaemia in cattle and buffalo. A polymerase chain reaction (PCR) assay was developed using primers derived from conserved part of 16S-23S rRNA gene. The PCR amplified a fragment size of 0.7 kb using DNA from nine avian P. multocida  isolates...

Secondary structure assignment.